//This function is used for sorting the paths for a query from best to worst.
//it uses < to mean 'better than'.
bool BlastQueryPath::operator<(BlastQueryPath const &other) const
{
//First we compare using the E-value product. This seems to value stronger
//hits as well as paths with fewer, longer hits.
SciNot aEValueProduct = getEvalueProduct();
SciNot bEValueProduct = other.getEvalueProduct();
if (aEValueProduct != bEValueProduct)
return aEValueProduct < bEValueProduct;
//If the code got here, then the two paths have the same e-value product,
//possibly because they contain the same hits, or possibly because they both
//contain hits so strong as to have an e-value of zero.
//Now we compare using mean percent identity.
double aMeanPercIdentity = getMeanHitPercIdentity();
double bMeanPercIdentity = other.getMeanHitPercIdentity();
if (aMeanPercIdentity != bMeanPercIdentity)
return aMeanPercIdentity > bMeanPercIdentity;
//Now we use the absolute value of the length discrepancy.
double aLengthDiscrepancy = fabs(getRelativeLengthDiscrepancy());
double bLengthDiscrepancy = fabs(other.getRelativeLengthDiscrepancy());
if (aLengthDiscrepancy != bLengthDiscrepancy)
return aLengthDiscrepancy < bLengthDiscrepancy;
//Now we use fraction of query covered by hits.
double aHitsQueryCoverage = getHitsQueryCoverage();
double bHitsQueryCoverage = other.getHitsQueryCoverage();
if (aHitsQueryCoverage != bHitsQueryCoverage)
return aHitsQueryCoverage > bHitsQueryCoverage;
return false;
}
QueryPathsDialog::QueryPathsDialog(QWidget * parent, BlastQuery * query) :
QDialog(parent),
ui(new Ui::QueryPathsDialog)
{
ui->setupUi(this);
setWindowFlags(windowFlags() | Qt::WindowStaysOnTopHint);
connect(this, SIGNAL(rejected()), this, SLOT(hidden()));
connect(ui->tableWidget, SIGNAL(itemSelectionChanged()), this, SLOT(tableSelectionChanged()));
g_memory->queryPathDialogIsVisible = true;
g_memory->queryPaths.clear();
ui->tableWidget->setHorizontalHeaderLabels(QStringList() << "Path" << "Length\n(bp)" << "Query\ncovered\nby path" <<
"Query\ncovered\nby hits" << "Mean hit\nidentity" << "Total\nhit mis-\nmatches" <<
"Total\nhit gap\nopens" << "Length\ndiscre-\npancy" << "E-value\nproduct");
QString queryDescription = "Query name: " + query->getName();
queryDescription += " type: " + query->getTypeString();
queryDescription += " length: " + formatIntForDisplay(query->getLength());
if (query->getSequenceType() == PROTEIN)
queryDescription += " (" + formatIntForDisplay(3 * query->getLength()) + " bp)";
else
queryDescription += " bp";
ui->queryLabel->setText(queryDescription);
ui->tableWidget->clearContents();
ui->tableWidget->setSortingEnabled(false);
int pathCount = query->getPathCount();
ui->tableWidget->setRowCount(pathCount);
if (pathCount == 0)
return;
QList<BlastQueryPath> paths = query->getPaths();
for (int i = 0; i < pathCount; ++i)
{
BlastQueryPath * queryPath = &paths[i];
QTableWidgetItem * pathString = new QTableWidgetItem(queryPath->getPath().getString(true));
pathString->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int length = queryPath->getPath().getLength();
TableWidgetItemInt * pathLength = new TableWidgetItemInt(formatIntForDisplay(length), length);
pathLength->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double queryCoveragePath = queryPath->getPathQueryCoverage();
TableWidgetItemDouble * pathQueryCoveragePath = new TableWidgetItemDouble(formatDoubleForDisplay(100.0 * queryCoveragePath, 2) + "%", queryCoveragePath);
pathQueryCoveragePath->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
pathLength->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double queryCoverageHits = queryPath->getHitsQueryCoverage();
TableWidgetItemDouble * pathQueryCoverageHits = new TableWidgetItemDouble(formatDoubleForDisplay(100.0 * queryCoverageHits, 2) + "%", queryCoverageHits);
pathQueryCoverageHits->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double percIdentity = queryPath->getMeanHitPercIdentity();
TableWidgetItemDouble * pathPercIdentity = new TableWidgetItemDouble(formatDoubleForDisplay(percIdentity, 2) + "%", percIdentity);
pathPercIdentity->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int mismatches = queryPath->getTotalHitMismatches();
TableWidgetItemInt * pathMismatches = new TableWidgetItemInt(formatIntForDisplay(mismatches), mismatches);
pathMismatches->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
int gapOpens = queryPath->getTotalHitGapOpens();
TableWidgetItemInt * pathGapOpens = new TableWidgetItemInt(formatIntForDisplay(gapOpens), gapOpens);
pathGapOpens->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double lengthDisc = queryPath->getRelativeLengthDiscrepancy();
QString lengthDiscSign = "";
if (lengthDisc > 0.0)
lengthDiscSign = "+";
TableWidgetItemDouble * pathLengthDisc = new TableWidgetItemDouble(lengthDiscSign + formatDoubleForDisplay(100.0 * lengthDisc, 2) + "%", lengthDisc);
pathLengthDisc->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
double evalueProduct = queryPath->getEvalueProduct();
TableWidgetItemDouble * pathEvalueProduct = new TableWidgetItemDouble(QString::number(evalueProduct), evalueProduct);
pathEvalueProduct->setFlags(Qt::ItemIsEnabled | Qt::ItemIsSelectable);
ui->tableWidget->setItem(i, 0, pathString);
ui->tableWidget->setItem(i, 1, pathLength);
ui->tableWidget->setItem(i, 2, pathQueryCoveragePath);
ui->tableWidget->setItem(i, 3, pathQueryCoverageHits);
ui->tableWidget->setItem(i, 4, pathPercIdentity);
ui->tableWidget->setItem(i, 5, pathMismatches);
ui->tableWidget->setItem(i, 6, pathGapOpens);
ui->tableWidget->setItem(i, 7, pathLengthDisc);
ui->tableWidget->setItem(i, 8, pathEvalueProduct);
}
ui->tableWidget->resizeColumns();
ui->tableWidget->setSortingEnabled(true);
ui->queryPathsInfoText->setInfoText("This table shows information about the possible paths through the graph which "
"represent the query. These paths can be either simple (residing within a single "
"node) or complex (spanning multiple nodes). The columns in the table are as "
"follows:"
"<br><br>"
"<b>Path</b>: This is the query path through the graph, as written in Bandage's "
"path notation. The nodes in the path are separated by commas. The start position "
"in the first node is shown in parentheses at the beginning of the path. The end "
"position in the last node is shown in parentheses at the end of the path."
"<br><br>"
"<b>Length</b>: This is the path length. It is shown in base pairs, whether the "
"query is a nucleotide query or a protein query."
"<br><br>"
"<b>Query covered by path</b>: This is the fraction of the query which is covered "
"by the path. It is calculated by taking 100% and subtracting the fraction of the "
"query which is not captured by the start and the fraction of the query which is "
"not captured by the end."
"<br><br>"
"<b>Query covered by hits</b>: This is the fraction of the query which is covered "
"by the BLAST hits in this path. Since a path may contain nodes or parts of nodes which "
"are not covered by BLAST hits, this value will be less than or equal to the 'Query "
"covered by path' value."
"<br><br>"
"<b>Mean hit identity</b>: This is the mean of the percent identity for the BLAST "
"hits in this path, weighted by the hits' lengths."
"<br><br>"
"<b>Total hit mismatches</b>: This is the sum of the mismatches for the BLAST hits "
"in this path."
"<br><br>"
"<b>Total hit gap opens</b>: This is the sum of the gap opens for the BLAST hits "
"in this path."
"<br><br>"
"<b>Length discrepancy</b>: This is the percent difference in the path length and "
"the appropriate length for the relecant fraction of the query. A positive value "
"indicates that the path is too long; a negative value indicates that the path is "
"too short."
"<br><br>"
"<b>E-value product</b>: This is the product of the e-values for the BLAST hits "
"in this path.");
}
